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Alterations of the three short open reading frames in the Rous sarcoma virus leader RNA modulate viral replication and gene expression.

The Rous sarcoma virus (RSV) leader RNA has three short open reading frames (ORF1 to ORF3) which are conserved in all avian sarcoma-leukosis retroviruses. Effects on virus propagation were determined following three types of alterations in the ORFs: (i) replacement of AUG initiation codons in order to prohibit ORF translation, (ii) alterations of the codon context around the AUG initiation codon to enhance translation of the normally silent ORF3, and (iii) elongation of the ORF coding sequences. Mutagenesis of the AUG codons for ORF1 and ORF2 (AUG1 and AUG2) singly or together delayed the onset of viral replication and cell transformation. In contrast, mutagenesis of AUG3 almost completely suppressed these viral activities. Mutagenesis of ORF3 to enhance its translation inhibited viral propagation. When the mutant ORF3 included an additional frameshift mutation which extended the ORF beyond the initiation site for the gag, gag-pol, and env proteins, host cells were initially transformed but died soon thereafter. Elongation of ORF1 from 7 to 62 codons led to the accumulation of transformation-defective virus with a delayed onset of replication. In contrast, viruses with elongation of ORF1 from 7 to 30 codons, ORF2 from 16 to 48 codons, or ORF3 from 9 to 64 codons, without any alterations in the AUG context, exhibited wild-type phenotypes. These results are consistent with a model that translation of the ORFs is necessary to facilitate virus production.

Animals↗

Nucleotide sequence of the vaccinia virus thymidine kinase gene and the nature of spontaneous frameshift mutations.

Nucleotide sequencing of a 1,300-base-pair vaccinia virus DNA segment previously shown to contain a thymidine kinase (TK) gene revealed an uninterrupted reading frame of 177 codons capable of producing a polypeptide with a molecular weight of 20,102. Mapping of the TK mRNA by primer extension indicated a unique 5' end that precedes the initiation codon by only six nucleotides. Multiple 3' ends within a 10-nucleotide region, about 30 nucleotides beyond the termination codon, were located by nuclease digestion of DNA-RNA hybrids, and the length of the TK transcript, exclusive of polyadenylate, was estimated to be approximately 570 nucleotides. The region preceding the TK mRNA start site is extremely A + T rich and has sequence homologies with three other early genes. Genetic information is so compressed in this region of the DNA that the putative transcriptional regulatory sequence of the TK gene overlaps the coding sequence of a late gene. Only nine nucleotides separate the termination codon of the late gene from the initiation codon of the TK gene. Downstream, 66 nucleotides separate the TK termination codon from the apparent initiation codon of another early gene. The nature of three independent TK- mutants was revealed by nucleotide sequencing. Each has a nucleotide reiteration leading to a +1 frameshift and a nonsense codon downstream. The location of one frameshift mutation provided evidence that the first ATG is used for initiation of protein synthesis.

Amino Acid Sequence↗

Ubiquitin-activating enzyme (E1) isoforms in lens epithelial cells: origin of translation, E2 specificity and cellular localization determined with novel site-specific antibodies.

Lens development and response to peroxide stress are associated with dramatic changes in protein ubiquitination, reflecting dynamic changes in activity of the ubiquitin-activating enzyme (E1). Two isoforms of E1 (E1A and E1B) have been identified in lens cells although only one E1 mRNA, containing three potential translational start sites, has been detected. Novel, site-specific antibodies to E1 were generated and the hypothesis that the two isoforms of E1 are translated from alternative initiation codons of a single mRNA was tested. Antibodies raised against E1A-N peptide (Met(1)to Cys(23)of E1A) reacted only with E1A by immunoblot and immunoprecipitation. Antibodies raised against E1B-N peptide (Met(1)to Glu(25)of E1B or Met(41)to Glu(65)of E1A) and E1AB-C peptide (His(1030)to Arg(1058)of E1A or His(990)to Arg(1018)of E1B) reacted with both E1A and E1B. These results indicate that (1) E1A and E1B contain the same C-terminal residues; (2) E1A contains the N terminal sequence of E1B; and (3) E1B does not contain the N terminal sequence of E1A. The two isoforms of lens E1 are therefore translated from a single mRNA. Specifically, E1A is translated from the first initiation codon, and E1B translated from the second initiation codon. E1A and E1B were affinity-purified, and their ability to 'charge' ubiquitin carrier proteins (E2s) with activated ubiquitin was compared in a cell-free system. E1A and E1B were indistinguishable with respect to charging different E2s. However, E1 immunolocalization studies with human lens epithelial cells indicate that E1A and E1B are preferentially localized to the nucleus and cytosol, respectively. This observation suggests that E1A and E1B ubiquitinate different proteins and serve different functions in intact cells.

Animals↗

Ribosome-initiator tRNA complex as an intermediate in translation initiation in Escherichia coli revealed by use of mutant initiator tRNAs and specialized ribosomes.

For functional studies of mutant Escherichia coli initiator tRNAs in vivo, we previously described a strategy based on the use of tRNA genes carrying an anticodon sequence change from CAU to CUA along with a mutant chloramphenicol acetyltransferase (CAT) gene carrying an initiation codon change from AUG to UAG. Surprisingly, under conditions where the mutant initiator tRNA is optimally active, the CAT gene with the UAG initiation codon produced more CAT protein (3- to 9-fold more depending on the conditions) than the wild-type CAT gene. Here we show that two new mutant CAT genes having GUC and AUC initiation codons also produce more of the CAT protein in the presence of the corresponding mutant initiator tRNAs. These results are most easily understood if assembly of the 30S ribosome-initiator tRNA-mRNA initiation complex in vivo proceeds with the 30S ribosome binding first to the initiator tRNA and then to the mRNA. In cells overproducing the mutant initiator tRNAs, most ribosomes would carry the mutant initiator tRNA and these ribosomes would select the mutant CAT mRNA over the other mRNAs.

Acylation↗

Molecular basis of beta-thalassemia minor in Taiwan.

The mutations producing beta-thalassemia minor in 227 Taiwanese were studied using the method of naturally and amplified created restriction sites. beta-Thalassemia minor was caused by one beta-globin gene mutation in most of the cases (225/227); only a few cases were caused by two gene mutation (2/227). The most common type of mutation was frameshift codon 41/42 (-TCTT) (93/227), followed in descending order by the C-->T substitution at nucleotide 654 of IVS-2 (83/227), the nonsense mutation A--T at codon 17 (22/227), the A-->T mutation at position -28 of the promotor region (12/227), the frameshift codon 27/28 (+C) (6/227), the initial codon mutation (ATG-->AGG) (5/227), and one each of the codon 71/72 (+A), IVS-1 nt 1 (G-->T), IVS-1 3' end (TAG-->GAG), and nonsense codon 43. In the two cases of the two-gene mutation, one was the nt 654 mutation with Hb Kaohsiung and another one was frameshift codon 41/42 with Hb Meinung. The first four mutations accounted for more than 90% of the mutations. The C-->T substitution at the nt 654 of IVS-2 and initial codon mutation in our study had a higher incidence than in other Southeast Asia areas. Comparison of clinical data in different types of beta-thalassemia showed that there were higher MCV and MCH levels in beta (+)-thalassemia.

Adolescent↗

Expression of active human DNA ligase I in Escherichia coli cells that harbor a full-length DNA ligase I cDNA construct.

A recombinant plasmid for expression of full-length human DNA ligase I (phLig-I) was constructed in a plasmid/phage chimeric vector, pTD-T7N, which was derived from pUC118 by oligonucleotide-directed mutagenesis. The insert contained a 2757-base pair coding sequence for a whole human DNA ligase I and an extra ACC codon adjacent to the ATG initiation codon. This ACC codon was required for achieving high levels of expression of full-length DNA ligase I in Escherichia coli strain BL21. The recombinant plasmid, which was designed to exploit the T7 late promoter and the ATG initiation codon for beta-galactosidase was transfected into E. coli BL21 cells that express T7 RNA polymerase. The recombinant clone produced relatively high levels of DNA ligase I with a molecular mass of 130 kDa, as estimated by SDS-polyacrylamide gel electrophoresis. The DNA ligase was purified to near-homogeneity by the two-step column chromatographic procedure from BLphLig-I cells that had been induced with isopropyl beta-D-thiogalactoside. The specific activity, chromatographic behavior, kinetic properties, molecular mass, and antigenicity of the recombinant human DNA ligase I were indistinguishable from those of purified mammalian DNA ligase I. Metabolically labeling experiments with 32P(i) indicate that the recombinant DNA ligase I was present as an enzyme-AMP reaction intermediate, but not as a phosphoprotein, in the E. coli cells.

Amino Acid Sequence↗

mRNA structures influencing translation in the yeast Saccharomyces cerevisiae.

The mRNA sequence and structures that modify and are required for translation of iso-1-cytochrome c in the yeast Saccharomyces cerevisiae were investigated with sets of CYC1 alleles having alterations in the 5' leader region. Measurements of levels of CYC1 mRNA and iso-1-cytochrome c in strains having single copies of altered alleles with nested deletions led to the conclusion that there is no specific sequence adjacent to the AUG initiator codon required for efficient translation. However, the nucleotides preceding the AUG initiator codon at positions -1 and -3 slightly modified the efficiency of translation to an order of preference similar to that found in higher cells. In contrast to large effects observed in higher eucaryotes, the magnitude of this AUG context effect in S. cerevisiae was only two- to threefold. Furthermore, introduction of hairpin structures in the vicinity of the AUG initiator codon inhibited translation, with the degree of inhibition related to the stability and proximity of the hairpin. These results with S. cerevisiae and published findings on other organisms suggest that translation in S. cerevisiae is more sensitive to secondary structures than is translation in higher eucaryotes.

Alleles↗

Human choline acetyltransferase mRNAs with different 5'-region produce a 69-kDa major translation product.

Choline acetyltransferase (ChAT, EC 2.3.1.6) is the biosynthetic enzyme for acetylcholine. We have previously shown that multiple ChAT mRNA species with different 5'-noncoding regions are expressed in the rat and mouse. However, the diversity of ChAT mRNA species in human has not completely been elucidated. In this work N1- and N2-type ChAT cDNAs were cloned from a human brain cDNA library and the N-exon located in the human ChAT gene. Polymerase chain reaction analysis indicates that four species of ChAT mRNAs (R-, N1-, N2- and M-types) are produced in human brain and spinal cord. In all human transcripts, the ATG initiation codon in the rat, mouse and pig was replaced by ACG, which does not serve as an initiation codon for translation. In vitro translation and mammalian expression analyses revealed that N1-, N2- and R-type mRNAs give rise to a single 69 kDa enzyme, while M-type mRNA produces both 82 and 69 kDa enzymes. The translation efficiency of M-type mRNA was lower than that of the other mRNA species. Moreover, the translation efficiency of human ChAT mRNAs was considerably lower than that of rat ChAT mRNA, suggesting that the ATG codons for human ChAT are unfavorable for translation initiation compared with the initiation codon for rat ChAT. These results provide rational explanations for the previous reports that human ChAT protein purified from the brain and placenta had 66-70 kDa molecular mass, and that ChAT activity in a single motor neuron of human was far lower than that of other vertebrates. Sequencing of monkey ChAT gene showed that the initiation ATG in rodent ChAT was also replaced by ACA in the monkey.

Alternative Splicing↗

Mechanism of translation of the bicistronic mRNA encoding human papillomavirus type 16 E6-E7 genes.

The transforming genes E6 and E7 of human papillomavirus (HPV) type 16 and other HPV types are expressed from a bicistronic mRNA with a characteristic spacing of 3 to 6 bp between the termination codon of E6 and the initiation codon of E7. Plasmid pSP64E6E7 which contains the reading frames of both E6 and E7 was constructed in order to study the expression of both proteins in a coupled transcription/rabbit reticulocyte translation system. Both E6 and E7 proteins were expressed simultaneously. This translation could be interfered with by antisense oligonucleotides corresponding to various regions of the transcript. Antisense oligonucleotides targeted at sequences flanking either side of the translation initiation codon of the E6 open reading frame were effective in inhibiting the synthesis of both proteins, whereas oligonucleotides complementary to the coding regions downstream of the first start codon showed either a considerably reduced effect or none at all. In particular, there was limited inhibition of E7 translation by antisense oligonucleotides flanking the translation start region of the E7 gene. In the presence of RNase H, it was possible to selectively inhibit the synthesis of either E6 or E7 by several gene-internal antisense oligonucleotides. We conclude that HPV16 E6-E7 bicistronic mRNA is fully functional and that both proteins are translated with equal efficiency via the scanning mechanisms with reinitiation at the second open reading frame. In addition, both AE6 and AE7 may have therapeutical potential as they are capable of inhibiting the proliferation of CaSki cells which contain the HPV16 genome.

Amino Acid Sequence↗

Calliper randomization: an artificial neural network based analysis of E. coli ribosome binding sites.

An artificial neural network based approach has been used in analyzing the translation initiation region of E. coli. The approach is based on using a trained network capable of recognizing a particular region and presenting the network with randomized calliper inputs of the true sequence. The network responds with an error when the regions which have been the main source of knowledge are randomized. Analysis of the E. coli ribosome binding sites using this approach reveal that the initiation codon and the Shine/Dalgarno sequence which are known to be important for translation initiation are also important in imparting knowledge to the network. Further, selectively changing the usually occurring initiation codon AUG, to GUG, UUG and AUU, which occur less frequently, decreases the network performance in accordance with the frequency of their occurrence. This approach can be used as a general method to derive consensus.

Binding Sites↗

Overexpression of a gene cluster encoding a chalcone synthase-like protein confers redbrown pigment production in Streptomyces griseus.

A 7.0-kb DNA fragment that conferred redbrown pigment production on Streptomyces griseus was shotgun-cloned with a multicopy vector pIJ486 from this microorganism. By restriction endonuclease mapping and subcloning, a 1.5-kb fragment which is essential for the production of redbrown pigment was determined. The nucleotide sequence of this region revealed the presence of two open reading frames, ORF1 with 109 amino acids (named RppA) and ORF2 with 262 amino acids (RppB), in addition to a truncated ORF3. The termination codon of rppA and the initiation codon of rppB overlapped, sharing one common nucleotide, which strongly suggests that these two genes are cotranscribed. Both rppA and rppB were essentially required for the pigmentation. The RppB protein showed great similarity in amino acid sequence to a chalcone synthase, a key enzyme of central importance in the biosynthetic pathway of all classes of flavonoids in plants. Part of RppA showed sequence similarity to the 33kDa phosphoprotein of adenovirus. Nucleotide sequences homologous to rppA and rppB were widely distributed in Streptomyces species, as determined by Southern hybridization. Further nucleotide sequencing of the entire orf-3 gene showed that ORF3 with 403 amino acids was a cytochrome P-450 (named P-450RPP). These data suggested that the cloned fragment contained part of a gene cluster for the biosynthesis of a certain metabolite. Introduction of the subcloned 1.5-kb fragment into Streptomyces lividans as well as Escherichia coli also caused production of redbrown pigment, suggesting that RppA and RppB are capable of synthesizing the redbrown pigment from metabolites commonly present in bacteria.

Acyltransferases↗

Regulation of ribonucleotide reductase M2 expression by the upstream AUGs.

Ribonucleotide reductase catalyzes a rate-limiting reaction in DNA synthesis by converting ribonucleotides to deoxyribonucleotides. It consists of two subunits and the small one, M2 (or R2), plays an essential role in regulating the enzyme activity and its expression is finely controlled. Changes in the M2 level influence the dNTP pool and, thus, DNA synthesis and cell proliferation. M2 gene has two promoters which produce two major mRNAs with 5'-untranslated regions (5'-UTRs) of different lengths. In this study, we found that the M2 mRNAs with the short (63 nt) 5'-UTR can be translated with high efficiency whereas the mRNAs with the long (222 nt) one cannot. Examination of the long 5'-UTR revealed four upstream AUGs, which are in the same reading frame as the unique physiological translation initiation codon. Further analysis demonstrated that these upstream AUGs act as negative cis elements for initiation at the downstream translation initiation codon and their inhibitory effect on M2 translation is eIF4G dependent. Based on the findings of this study, we conclude that the expression of M2 is likely regulated by fine tuning the translation from the mRNA with a long 5'-UTR during viral infection and during the DNA replication phase of cell proliferation.

5' Untranslated Regions↗

The translational and transcriptional initiation sites of BmNPV lef-7 gene.

The predicted open reading frame of lef-7 from Bombyx mori nucleopolyhedrovirus (BmNPV) is 45 bp longer at the 5'-terminal and harbors a 42 bp deletion towards the 3' terminal end compared to that of Autograph californica mlulticapsid NPV (AcMNPV). In the present study, to determine whether the BmNPV lef-7 is translated from an initiation site different from that of AcMNPV lef-7, the translational and transcriptional initiation sites of BmNPV lef-7 were examined. A BmNPV mutant, Bmlef7M1(-) was constructed by deleting 11 nucleotides (nt) including the predicted initiation codon ATG. Western blot analysis demonstrated that the size of LEF-7 in BmNPV and Bmlef7M1(-)-infected cells was identical. The LEF-7s in BmNPV and Bmlef7M1(-)-infected cells were both localized in the nuclei as observed using confocal microscopy. Therefore, the presumed initiation codon ATG (at 97059 nt of BmNPV genome) appears to be non-functional for lef-7 translation. The 5'-RACE analysis revealed that transcription of lef-7 mRNA in BmNPV and Bmlef7M1(-)-infected cells both initiated from an ATCATT motif located 26 nt upstream of the second ATG (located at 97014 nt on BmNPV genome), and 20 nt downstream of the presumed initiation codon.

Animals↗

The complete nucleotide sequence and gene organization of the mitochondrial genome of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae).

The complete nucleotide sequences of the mitochondrial genome (mitogenome) of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae), were determined. The 15,521-bp-long G. orientalis mitogenome contains typical gene complement, base composition, and codon usage found in metazoan mitogenomes. The G. orientalis mitogenome contains the third lowest A+T content (70.5%) among the complete insects mt genome sequences. The initiation codon for the G. orientalis COI gene appears to be ATG, instead of the tetranucleotides, which have been postulated to act as initiation codon for Locusta migratoria and some lepidopteran COI genes. The initiation codon for ND2 appears to be GTG, which is rare, but has been designated as an initiator of Tricholepidion gertschi ND2. All anticodons of G. orientalis tRNAs were identical to Drosophila yakuba and L. migratoria. The tRNA(Ser)(AGN) could not form a stable stem loop structure in the DHU arm as shown in many other insect tRNA(Ser)(AGN). Phylogenetic analysis of nucleotide sequence information from all mt genes supported a monophyletic Diptera, a monophyletic Lepidoptera, a monophyletic Coleoptera, a monophyletic Mecopterida (Diptera+Lepidoptera), and a monophyletic Endopterygota (Diptera+Lepidoptera+Coleoptera), suggesting that the complete insect mitogenome sequence has a resolving power to the diversification events within Endopterygota. However, the relationships of ancient insect orders were unstable, indicating the limited use of mitogenome information at deeper phylogenetic depth.

Animals↗

An aminoterminally extended P1-protamine variant in the boar.

We have found a minor form of boar sperm P1-protamine with a six amino acid long N-terminal extension. When this sequence was compared with the recently published gene sequence of boar P1-protamine, and with DNA sequences obtained from the boars studied here, a perfect match was found with the 5'-region upstream of the ATG initiation codon of the authentic P1-protamine. Since no extra in-frame ATG initiation codons are present in the 5'-region of the gene, we conclude that the translation of boar P1-protamine variant starts with a non-AUG initiation codon, CUG, which precedes the codon of the first amino acid (serine) of the sequenced variant.

Amino Acid Sequence↗

Identification and characterization of the products from the traJ and traY genes of plasmid R100.

The nucleotide sequence of part of the tra region of R100 including traJ and traY was determined, and the products of several tra genes were identified. The nucleotide sequence of traJ, encoding a protein of 223 amino acids, showed poor homology with the corresponding segments of other plasmids related to R100, but the deduced amino acid sequences showed low but significant homology. The first four amino acids at the N-terminal region of the TraJ protein were not essential for positive regulation of expression of traY, the first gene of the traYZ operon. The nucleotide sequence of traY shows that this gene may use TTG as the initiation codon and that it encodes a protein of 75 amino acids. Analysis of the traY gene product, which was obtained as the fusion protein with beta-galactosidase, showed that the N-terminal region of the product has an amino acid sequence identical to that deduced from the assigned frame but lacks formylmethionine. traY of plasmid F, which encodes a larger protein than the TraY protein of R100, is thought to use ATG as an initiation codon. However, a TTG initiation codon was found in the preceding region of the previously assigned traY coding frame of F. Interestingly, when translation of traY of F was initiated from TTG, the amino acid sequence homologous to the TraY protein of R100 appeared in tandem in the TraY protein of F. This may suggest that traY of F has undergone duplication of a gene like the traY gene of R100.

Amino Acid Sequence↗

Nucleotide sequence comparisons of plasmids pHD131, pJB1, pFA3, and pFA7 and beta-lactamase expression in Escherichia coli, Haemophilus influenzae, and Neisseria gonorrhoeae.

The sites of initiation for beta-lactamase mRNA transcription and the nucleotide sequences of beta-lactamase plasmids derived from Haemophilus and Neisseria species were determined. In N. gonorrhoeae, transcription from plasmid pFA3 was initiated from two sites, one located about 20 base pairs (bp) and the other 210 bp upstream of the beta-lactamase initiating codon, whereas in H. influenzae, transcriptional initiation from plasmid pHD131 occurred at two different sites, approximately 150 and 170 bp upstream of the initiating codon. When these plasmids were transformed into Escherichia coli, transcription was initiated at the 150- and 170-bp upstream sites in both plasmids. The nucleotide sequences of both plasmids within the noncoding region upstream of the transcriptional initiation site were identical and, except at two or three nucleotide positions, the sequences were also identical to the corresponding region of Tn3. At one of these positions there is a TA for CG substitution, which correlates in E. coli and Haemophilus sp. with the presence of two strong, overlapping beta-lactamase promoters, initiating transcription at the 150- and 170-bp upstream sites. Over a larger (875-bp) segment comprising most of the sequences of the tnpR and bla genes, the nucleotide sequences of both plasmids were also identical, and although this sequence differed from the corresponding Tn3 sequence at 18 sites, it was identical to that of Tn2, except at one site. The sequence of a second Haemophilus plasmid, pJB1, was identical to that of pHD131 in the same region, except at two nucleotides. All three plasmids were identical in nucleotide sequence in other TnA regions, as well as in regions flanking the TnA sequence, except that the Neisseria plasmid lacked a TnA segment of 3,298 bp [comprising the IR(L) and proximal sequences] together with approximately 273 bp of the non-TnA region adjacent to IR(L). The sequence of a second N. gonorrhoeae plasmid, pFA7, was identical to pFA3, except that the terminal, 3,299 TnA nucleotides were missing.

Base Sequence↗

Human liver glucokinase gene: cloning and sequence determination of two alternatively spliced cDNAs.

A human liver glucokinase (ATP:D-hexose 6-phosphotransferase, EC 2.7.1.1) cDNA was isolated from a liver cDNA library. This cDNA (hLGLK1) appeared to be full length [2548 base pairs (bp) plus additional poly(A) residues], as its size was consistent with a single 2.8-kilobase (kb) glucokinase mRNA on Northern blot analysis of liver poly(A)+ RNA. The cDNA contained an open reading frame of 1392 bp that predicted a protein of 464 amino acids and a molecular mass of 52 kDa; this protein has 97% identity to rat liver glucokinase. Fourteen residues on the amino terminus of the predicted human liver glucokinase, however, differed completely from those of the predicted rat liver enzyme and could be explained by alternative splicing of a 124-bp cassette exon in human cDNA. A second glucokinase cDNA (hLGLK2), missing the 124-bp cassette exon, was isolated by PCR amplification of human liver cDNA. The hLGLK2 cDNA contained an open reading frame of 1398 bp from an ATG codon at position 164, encoding a predicted protein of 466 residues, 98% identical to the rat enzyme, but different from the predicted protein of hLGLK1 cDNA by 16 amino-terminal residues. In contrast, hLGLK1 cDNA contains multiple initiator codons upstream of the predicted initiator codon at position 294 within the cassette exon. Translation of the two mRNAs in vitro by a reticulocyte lysate system resulted in proteins of the expected size (52 kDa) for both mRNAs; yet hLGLK2 mRNA was translated four to six times more efficiently. These results suggested that the alternative splicing of a cassette exon in hLGLK1 resulted in an mRNA with an upstream initiator codon and reduced function. The relative biological activity of the two isoforms of human glucokinase and their possible developmental and/or metabolic regulation remain to be determined.

Amino Acid Sequence↗